How do I change this to “idiomatic” Perl?

Question

I am beginning to delve deeper into Perl, but am having trouble writing \"Perl-ly\" code instead of writing C in Perl. How can I change the following code to use more Perl idiom

Answer 1

I would always advise to look at CPAN for previous solutions or examples of how to do things in Perl. Have you looked at Algorithm::NeedlemanWunsch?

The documentation to this module includes an example for matching DNA sequences. Here is an example using the similarity matrix from wikipedia.

#!/usr/bin/perl -w
use strict;
use warnings;
use Inline::Files;                 #multiple virtual files inside code
use Algorithm::NeedlemanWunsch;    # refer CPAN - good style guide

# Read DNA sequences
my @a = read_DNA_seq("DNA_SEQ_A");
my @b = read_DNA_seq("DNA_SEQ_B");

# Read Similarity Matrix (held as a Hash of Hashes)
my %SM = read_Sim_Matrix();

# Define scoring based on "Similarity Matrix" %SM
sub score_sub {
    if ( !@_ ) {
        return -3;                 # gap penalty same as wikipedia)
    }
    return $SM{ $_[0] }{ $_[1] };    # Similarity Value matrix
}

my $matcher = Algorithm::NeedlemanWunsch->new( \&score_sub, -3 );
my $score = $matcher->align( \@a, \@b, { align => \&check_align, } );

print "\nThe maximum score is $score\n";

sub check_align {
    my ( $i, $j ) = @_;              # @a[i], @b[j]
    print "seqA pos: $i, seqB pos: $j\t base \'$a[$i]\'\n";
}

sub read_DNA_seq {
    my $source = shift;
    my @data;
    while (<$source>) {
        push @data, /[ACGT-]{1}/g;
    }
    return @data;
}

sub read_Sim_Matrix {

    #Read DNA similarity matrix (scores per Wikipedia)
    my ( @AoA, %HoH );
    while () {
        push @AoA, [/(\S+)+/g];
    }

    for ( my $row = 1 ; $row < 5 ; $row++ ) {
        for ( my $col = 1 ; $col < 5 ; $col++ ) {
            $HoH{ $AoA[0][$col] }{ $AoA[$row][0] } = $AoA[$row][$col];
        }
    }
    return %HoH;
}

__DNA_SEQ_A__
A T G T A G T G T A T A G T
A C A T G C A
__DNA_SEQ_B__
A T G T A G T A C A T G C A
__SIMILARITY_MATRIX__
-  A  G  C  T
A  10  -1  -3  -4
G  -1  7  -5  -3
C  -3  -5  9  0
T  -4  -3  0  8

And here is some sample output:

seqA pos: 7, seqB pos: 2  base 'G'
seqA pos: 6, seqB pos: 1  base 'T'
seqA pos: 4, seqB pos: 0  base 'A'

The maximum score is 100